Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: ZV21N

Calculation Name: 3UKN-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UKN

Chain ID: C

ChEMBL ID:

UniProt ID: A8WHX9

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2172163.756762
FMO2-HF: Nuclear repulsion 2094085.000972
FMO2-HF: Total energy -78078.75579
FMO2-MP2: Total energy -78305.493179


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(C:549:ARG)


Summations of interaction energy for fragment #1(C:549:ARG)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-75.739-73.32421.075-11.352-12.138-0.114
Interaction energy analysis for fragmet #1(C:549:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.915 / q_NPA : 0.938
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3C551LEU00.0450.0263.8932.1053.477-0.013-0.643-0.7170.002
4C552TYR00.0290.0356.5832.6142.6140.0000.0000.0000.000
5C553HIS00.0280.0164.5172.5752.675-0.001-0.005-0.0930.000
6C554THR0-0.018-0.0234.7201.2581.337-0.001-0.004-0.0740.000
7C555ARG10.8420.9076.89822.34322.3430.0000.0000.0000.000
8C556THR0-0.024-0.0219.9302.0172.0170.0000.0000.0000.000
9C557LYS10.8100.8858.87318.27318.2730.0000.0000.0000.000
10C558ASP-1-0.828-0.89310.968-18.254-18.2540.0000.0000.0000.000
11C559LEU00.0030.00512.9351.0811.0810.0000.0000.0000.000
12C560LYS10.9430.96513.12516.57916.5790.0000.0000.0000.000
13C561ASP-1-0.789-0.87414.643-14.150-14.1500.0000.0000.0000.000
14C562PHE00.0210.01616.7390.6570.6570.0000.0000.0000.000
15C563ILE00.003-0.00418.6370.6250.6250.0000.0000.0000.000
16C564ARG10.8860.94016.91713.47013.4700.0000.0000.0000.000
17C565VAL0-0.026-0.02519.8130.5190.5190.0000.0000.0000.000
18C566HIS0-0.016-0.00522.4410.5750.5750.0000.0000.0000.000
19C567ARG10.8380.92424.38910.23810.2380.0000.0000.0000.000
20C568LEU00.0410.02623.7710.2840.2840.0000.0000.0000.000
21C569PRO00.0290.02625.081-0.188-0.1880.0000.0000.0000.000
22C570LYS10.9690.96722.35210.97310.9730.0000.0000.0000.000
23C571ALA00.0240.00525.291-0.244-0.2440.0000.0000.0000.000
24C572LEU0-0.012-0.00425.515-0.022-0.0220.0000.0000.0000.000
25C573ALA00.0430.01321.622-0.274-0.2740.0000.0000.0000.000
26C574GLN0-0.0080.00321.216-0.379-0.3790.0000.0000.0000.000
27C575ARG10.9770.98722.2599.1359.1350.0000.0000.0000.000
28C576MET0-0.0150.00420.616-0.068-0.0680.0000.0000.0000.000
29C577LEU00.001-0.00416.054-0.490-0.4900.0000.0000.0000.000
30C578GLU-1-0.814-0.89918.217-13.104-13.1040.0000.0000.0000.000
31C579CYS0-0.0140.00420.809-0.045-0.0450.0000.0000.0000.000
32C580PHE0-0.024-0.01512.038-0.103-0.1030.0000.0000.0000.000
33C581GLN0-0.014-0.01716.212-1.266-1.2660.0000.0000.0000.000
34C582THR0-0.024-0.02517.236-0.254-0.2540.0000.0000.0000.000
35C583THR0-0.041-0.02319.1470.2980.2980.0000.0000.0000.000
36C584TRP0-0.048-0.01510.0060.4090.4090.0000.0000.0000.000
37C585SER0-0.006-0.01115.3430.1230.1230.0000.0000.0000.000
38C586VAL00.0200.02210.1540.0410.0410.0000.0000.0000.000
39C587ASN00.003-0.00212.683-0.247-0.2470.0000.0000.0000.000
40C588ASN0-0.059-0.04615.5560.3120.3120.0000.0000.0000.000
41C589GLY00.0140.00612.9200.7540.7540.0000.0000.0000.000
42C590ILE0-0.0150.00510.663-1.193-1.1930.0000.0000.0000.000
43C591ASP-1-0.771-0.8438.535-22.654-22.6540.0000.0000.0000.000
44C592VAL0-0.024-0.02410.547-0.142-0.1420.0000.0000.0000.000
45C593SER0-0.038-0.03511.3940.9470.9470.0000.0000.0000.000
46C594GLU-1-0.761-0.87413.811-16.586-16.5860.0000.0000.0000.000
47C595LEU0-0.014-0.01811.6710.8760.8760.0000.0000.0000.000
48C596LEU00.0410.03215.1920.3560.3560.0000.0000.0000.000
49C597LYS10.8000.90218.05314.53314.5330.0000.0000.0000.000
50C598ASP-1-0.889-0.95120.569-12.434-12.4340.0000.0000.0000.000
51C599PHE0-0.036-0.01018.4510.2860.2860.0000.0000.0000.000
52C600PRO00.0260.01223.0590.1780.1780.0000.0000.0000.000
53C601ASP-1-0.838-0.94224.360-13.421-13.4210.0000.0000.0000.000
54C602GLU-1-0.918-0.94923.863-11.876-11.8760.0000.0000.0000.000
55C603LEU00.0020.00320.606-0.371-0.3710.0000.0000.0000.000
56C604ARG10.8170.90619.71113.63313.6330.0000.0000.0000.000
57C605ALA00.011-0.00119.133-0.941-0.9410.0000.0000.0000.000
58C606ASP-1-0.871-0.94319.681-15.966-15.9660.0000.0000.0000.000
59C607ILE00.0090.00914.514-1.001-1.0010.0000.0000.0000.000
60C608ALA00.0150.00814.943-1.325-1.3250.0000.0000.0000.000
61C609MET0-0.064-0.02715.811-0.299-0.2990.0000.0000.0000.000
62C610HIS0-0.056-0.00713.457-0.115-0.1150.0000.0000.0000.000
63C611LEU0-0.078-0.0269.787-2.660-2.6600.0000.0000.0000.000
64C612ASN0-0.021-0.02510.6911.9851.9850.0000.0000.0000.000
65C613LYS10.8780.9447.81631.59331.5930.0000.0000.0000.000
66C614GLU-1-0.742-0.8606.875-36.867-36.8670.0000.0000.0000.000
67C615LEU0-0.026-0.00310.3631.8001.8000.0000.0000.0000.000
68C616LEU0-0.046-0.03412.2791.4551.4550.0000.0000.0000.000
69C617GLN0-0.070-0.03812.2371.1651.1650.0000.0000.0000.000
70C618LEU0-0.0360.00814.0730.5480.5480.0000.0000.0000.000
71C619PRO00.0910.02917.3470.2750.2750.0000.0000.0000.000
72C620LEU0-0.0120.02819.9540.4680.4680.0000.0000.0000.000
73C621PHE0-0.063-0.02916.9160.2940.2940.0000.0000.0000.000
74C622GLU-1-0.926-0.94520.653-12.241-12.2410.0000.0000.0000.000
75C623SER0-0.011-0.01822.9670.3030.3030.0000.0000.0000.000
76C624ALA0-0.049-0.01121.5540.3510.3510.0000.0000.0000.000
77C625SER00.014-0.02023.614-0.194-0.1940.0000.0000.0000.000
78C626ARG10.9030.93822.88612.66412.6640.0000.0000.0000.000
79C627GLY00.0260.02023.223-0.403-0.4030.0000.0000.0000.000
80C628CYS0-0.0160.01922.311-0.606-0.6060.0000.0000.0000.000
81C629LEU00.0610.02518.088-0.751-0.7510.0000.0000.0000.000
82C630ARG10.8640.93215.70616.81616.8160.0000.0000.0000.000
83C631SER00.0290.00617.797-0.693-0.6930.0000.0000.0000.000
84C632LEU00.001-0.00616.540-0.525-0.5250.0000.0000.0000.000
85C633SER0-0.051-0.03813.572-1.349-1.3490.0000.0000.0000.000
86C634LEU0-0.0020.00112.840-2.045-2.0450.0000.0000.0000.000
87C635ILE0-0.061-0.02214.122-0.396-0.3960.0000.0000.0000.000
88C636ILE0-0.0220.0089.250-0.341-0.3410.0000.0000.0000.000
89C637LYS10.7750.8938.59221.46021.4600.0000.0000.0000.000
90C638THR00.0310.0014.046-0.862-0.5150.000-0.038-0.3080.000
91C639SER0-0.052-0.0364.0453.1453.372-0.001-0.036-0.1920.000
92C640PHE0-0.0070.0042.233-2.963-1.1773.441-1.699-3.527-0.009
93C641CYS0-0.047-0.0274.0834.5124.6230.002-0.056-0.0580.000
94C642ALA00.0550.0167.371-0.593-0.5930.0000.0000.0000.000
95C643PRO00.003-0.0169.6990.6170.6170.0000.0000.0000.000
96C644GLY00.0120.01913.1131.2301.2300.0000.0000.0000.000
97C645GLU-1-0.840-0.9019.264-25.586-25.5860.0000.0000.0000.000
98C646PHE00.0180.00413.269-0.157-0.1570.0000.0000.0000.000
99C647LEU00.0280.01411.311-0.842-0.8420.0000.0000.0000.000
100C648ILE0-0.009-0.01914.0230.1160.1160.0000.0000.0000.000
101C649ARG10.8270.90817.68114.88314.8830.0000.0000.0000.000
102C650GLN00.0330.02421.0870.2440.2440.0000.0000.0000.000
103C651GLY00.0250.01924.4230.4390.4390.0000.0000.0000.000
104C652ASP-1-0.782-0.86819.924-14.175-14.1750.0000.0000.0000.000
105C653ALA0-0.039-0.01222.9340.2080.2080.0000.0000.0000.000
106C654LEU00.0320.02119.009-0.516-0.5160.0000.0000.0000.000
107C655GLN0-0.020-0.00617.0640.2900.2900.0000.0000.0000.000
108C656ALA0-0.036-0.02614.863-0.082-0.0820.0000.0000.0000.000
109C657ILE00.0260.03415.9830.8330.8330.0000.0000.0000.000
110C658TYR0-0.023-0.04311.949-1.522-1.5220.0000.0000.0000.000
111C659PHE00.0660.0369.2401.1841.1840.0000.0000.0000.000
112C660VAL00.0180.0129.370-3.540-3.5400.0000.0000.0000.000
113C661CYS0-0.0080.0085.5461.0191.0190.0000.0000.0000.000
114C662SER0-0.062-0.0465.7901.8371.8370.0000.0000.0000.000
115C663GLY00.0650.0228.336-0.963-0.9630.0000.0000.0000.000
116C664SER0-0.031-0.02510.4871.5161.5160.0000.0000.0000.000
117C665MET0-0.005-0.00510.945-0.668-0.6680.0000.0000.0000.000
118C666GLU-1-0.769-0.87115.246-13.994-13.9940.0000.0000.0000.000
119C667VAL00.0120.00518.510-0.577-0.5770.0000.0000.0000.000
120C668LEU00.0150.00720.9800.6430.6430.0000.0000.0000.000
121C669LYS10.8630.93223.77110.52210.5220.0000.0000.0000.000
122C670ASP-1-0.880-0.93426.878-10.115-10.1150.0000.0000.0000.000
123C671ASN0-0.027-0.02827.039-0.142-0.1420.0000.0000.0000.000
124C672THR0-0.011-0.01126.666-0.386-0.3860.0000.0000.0000.000
125C673VAL0-0.017-0.01023.6350.1960.1960.0000.0000.0000.000
126C674LEU0-0.0330.00224.4890.4080.4080.0000.0000.0000.000
127C675ALA0-0.004-0.00621.7210.1420.1420.0000.0000.0000.000
128C676ILE0-0.015-0.01518.613-0.218-0.2180.0000.0000.0000.000
129C677LEU0-0.0200.00315.8260.2920.2920.0000.0000.0000.000
130C678GLY00.018-0.01513.438-0.488-0.4880.0000.0000.0000.000
131C679LYS10.8510.9188.63729.96929.9690.0000.0000.0000.000
132C680GLY00.0310.02412.143-0.800-0.8000.0000.0000.0000.000
133C681ASP-1-0.773-0.84314.196-17.123-17.1230.0000.0000.0000.000
134C682LEU00.003-0.00113.864-1.922-1.9220.0000.0000.0000.000
135C683ILE00.000-0.00314.2851.1571.1570.0000.0000.0000.000
136C684GLY00.029-0.00316.847-0.833-0.8330.0000.0000.0000.000
137C685SER0-0.033-0.02119.5570.7020.7020.0000.0000.0000.000
138C686ASP-1-0.796-0.88223.240-11.439-11.4390.0000.0000.0000.000
139C687SER00.0530.02226.0400.0110.0110.0000.0000.0000.000
140C688LEU0-0.035-0.00921.6410.1210.1210.0000.0000.0000.000
141C689THR0-0.027-0.02725.739-0.057-0.0570.0000.0000.0000.000
142C690LYS10.8650.90628.65910.72810.7280.0000.0000.0000.000
143C691GLU-1-0.706-0.83429.085-10.331-10.3310.0000.0000.0000.000
144C692GLN00.0610.02124.964-0.007-0.0070.0000.0000.0000.000
145C693VAL0-0.055-0.02227.8790.1630.1630.0000.0000.0000.000
146C694ILE0-0.0220.00324.103-0.434-0.4340.0000.0000.0000.000
147C695LYS10.8710.93724.78310.68610.6860.0000.0000.0000.000
148C696THR00.0150.00221.1890.2510.2510.0000.0000.0000.000
149C697ASN0-0.004-0.00324.421-0.127-0.1270.0000.0000.0000.000
150C698ALA00.0400.02423.4810.4270.4270.0000.0000.0000.000
151C699ASN0-0.028-0.02421.044-0.456-0.4560.0000.0000.0000.000
152C700VAL00.0010.00415.7160.0930.0930.0000.0000.0000.000
153C701LYS10.8540.91715.66014.90814.9080.0000.0000.0000.000
154C702ALA00.0100.01211.740-0.007-0.0070.0000.0000.0000.000
155C703LEU0-0.0050.00913.7340.9820.9820.0000.0000.0000.000
156C704THR0-0.038-0.02411.5360.6550.6550.0000.0000.0000.000
157C705TYR00.0140.0137.440-0.334-0.3340.0000.0000.0000.000
158C706CYS0-0.045-0.0037.6551.2951.2950.0000.0000.0000.000
159C707ASP-1-0.854-0.9121.749-125.856-127.55317.649-8.860-7.092-0.107
160C708LEU0-0.009-0.0014.7016.2166.306-0.001-0.011-0.0770.000
161C709GLN0-0.001-0.0295.382-1.559-1.5590.0000.0000.0000.000
162C710TYR00.0160.0007.7024.0794.0790.0000.0000.0000.000
163C711ILE00.0400.03311.519-0.572-0.5720.0000.0000.0000.000
164C712SER00.0080.00014.6511.4021.4020.0000.0000.0000.000
165C713LEU00.0380.00016.4610.4410.4410.0000.0000.0000.000
166C714LYS10.8210.91817.82116.30416.3040.0000.0000.0000.000
167C715GLY00.0430.02318.6020.5110.5110.0000.0000.0000.000
168C716LEU00.0350.01718.8390.2940.2940.0000.0000.0000.000
169C717ARG10.8720.93920.56511.91411.9140.0000.0000.0000.000
170C718GLU-1-0.831-0.87622.443-11.518-11.5180.0000.0000.0000.000
171C719VAL00.0380.00820.1850.4600.4600.0000.0000.0000.000
172C720LEU0-0.025-0.00923.2580.4850.4850.0000.0000.0000.000
173C721ARG10.7680.84125.49111.98411.9840.0000.0000.0000.000
174C722LEU0-0.0120.00825.0610.4020.4020.0000.0000.0000.000
175C723TYR00.0200.01224.2990.2320.2320.0000.0000.0000.000
176C724PRO00.0200.00527.658-0.122-0.1220.0000.0000.0000.000
177C725GLU-1-0.826-0.89928.747-10.892-10.8920.0000.0000.0000.000
178C726TYR00.021-0.00621.888-0.062-0.0620.0000.0000.0000.000
179C727ALA00.006-0.00426.246-0.128-0.1280.0000.0000.0000.000
180C728GLN0-0.029-0.01627.291-0.010-0.0100.0000.0000.0000.000
181C729LYS10.8990.96627.49110.52310.5230.0000.0000.0000.000
182C730PHE00.0200.00920.003-0.103-0.1030.0000.0000.0000.000
183C731VAL0-0.034-0.03524.971-0.188-0.1880.0000.0000.0000.000
184C732SER0-0.067-0.05727.1020.0520.0520.0000.0000.0000.000
185C733GLU-1-0.888-0.94126.636-10.711-10.7110.0000.0000.0000.000
186C734ILE0-0.047-0.01122.111-0.427-0.4270.0000.0000.0000.000
187C735GLN0-0.067-0.06123.165-0.543-0.5430.0000.0000.0000.000
188C736HIS0-0.0120.00324.9520.0280.0280.0000.0000.0000.000
189C737ASP-1-0.843-0.92319.385-16.020-16.0200.0000.0000.0000.000
190C738LEU0-0.069-0.02419.385-0.923-0.9230.0000.0000.0000.000
191C739THR0-0.020-0.03518.5530.5730.5730.0000.0000.0000.000
192C740TYR0-0.029-0.03619.8420.5340.5340.0000.0000.0000.000
193C741ASN00.0390.01920.861-0.542-0.5420.0000.0000.0000.000
194C742LEU00.0130.00919.3730.3690.3690.0000.0000.0000.000
195C743ARG10.8730.92923.83610.70810.7080.0000.0000.0000.000